The PSI-BLAST program can use both multiple alignments in the simple
alignment format similar to the one used by HMMeR, as well as binary
files, called checkpoints (*.c) or profiles. These profiles are
currently to be used on the command line and work with UNIX but not PC
implementations of PSI-BLAST. The best way to use them is by invoking
them using the perl scripts from the SEALS package of D. Roland
Walker(Ismb 1997;5:333-9) ), unless you want to or have your own scripts for the purpose.
The basic command line for using the profiles without any additional scripts is:
blastpgp -i <input query sequence> -d <database> -j <number of iterations> -R <*.c (the profile filename)> -o <output file>
If you are using SEALS the command is:
cat <input query sequence> |splishpgp <database> -j <number of iterations> -R <*.c (the profile filename)> -include_treshold= <e-value> |psi2normal|less
For P-loop ATPase, Helicases, WD40, von Willebrand A, TPRs, b-zips do not run the profiles to convergence. Case by case callibration of the iterations for a given database is a must.
The individual files contain the query sequences, and those with
.c suffix
are the binary profiles. You may open them carefully excise out the
query. Look at the query in the profile to ascertain whether or not
you are to use filtering by SEG.
If you have further questions regarding these profiles please contact
Eugene Koonin or L. Aravind.
http://genome-www.stanford.edu/yeast-worm/
The SGD team Last Modified: 12-11-1998
